50mm at f1.8 gives a very shallow depth of field if you're shooting anything reasonably close. Even slightly recomposing or the subject moving ever so slightly could be the culprit. Live view can help for critical focussing but I only ever use that with a tripod myself.

using the 50 at 1.8 makes it often very tricky to get everything in focus as the dof is so shallow.
Also, at least with my 50 it focuses in front of the subject when the subject is close, typically under a 1meter or so, after that its pretty good.
Also you may have moved slightly forwards or backwards, it will only take 1cm and you could be out.
The size of dof can be calculated if you google dof calculator.

1.8 is such a wide aperture, that it's pretty hard to tell what's in and out of focus using your DSLR's viewfinder. Modern DSLR viewfinders aren't really designed to focus anything larger than f/2, they're generally too small and dim. About a week ago when I was shooting at a banquet with my 50mm f/2 (Manual Focus Only) in very dim light, and I found it pretty much impossible to focus through the viewfinder. I needed the larger, brighter, easier to see screen where I could magnify the image to get a precise focus, and even that was difficult.

I personally use my display for Live View only where manual focusing is critical, otherwise I prefer the viewfinder. On occasions, I use live view for macro shots, especially when I'm at an awkward angle but overall I don't use it very often. The contrast based AF system is just too slow and I can't (of course) see the screen for my live in bright daylight.

I think you have to remember that the focussing screen on your camera is more about a brighter view than accurate manual focussing. If manual focussing is a priority the consider one of Canon's pro or semi-pro models which, with the exception of the 7D, have the option of interchangeable focussing screens.

For example, if I were looking for the best manual focussing option for my 5D2 whilst using fast lenses I'd buy a "Focusing Screen Eg-S Manual Precision Matte" which, from the Warehouse Express write-up, "is designed for manual focusing with high-speed lenses (f/2.8 or faster). The Eg-S screen has finer microlenses than the Ee-A or Eg-D along with a steeper parabola of focus to make the image pop in and out of focus more vividly in the viewfinder. However, the Eg-S focusing screen is not recommended for slower lenses because it's not very bright."

Interchangeable screens are cheap enough but that can't be said of the cameras that take them, I'm afraid.

You asked above if Sony uses a different system for their DSLRs. If you mean for the viewfinder itself...no - Sony's DSLRs use either a mirror or pentaprism, the same as other DSLRs. Sony do have models known as the SLTs - those use an electronic viewfinder feeding off the main sensor just like live view on your camera - but without any delay or having to switch back or flip mirrors, so these do operate quite differently.

If you are referring to live view systems, then yes - Sony uses a very different system than any other brand. Sony's live view on their DSLRs has multiple modes, one of which is 'quick AF' mode - in this mode, the camera switches to live view using a second sensor mounted up by the viewfinder and a slight deviation in the mirror angle to obtain a live view feed while maintaining the same normal phase-detect focus and shooting performance. In this mode, you can focus and shoot identically fast whether in live view or optical viewfinder, even up to 7 frames per second burst mode. They have a second live view mode working off the main sensor that works like the other brands, feeding off the main sensor and using contrast-detect focus (slower) and long pauses or delays for the shutter trigger waiting for mirrors to move or focus to confirm.

It is at least one way in which the Sony live view system is really the only one meant to be used for every-day casual shooting, or handheld shots, rather than tripod-mounted, fine-tuning type still subject shots. Be it in their SLT systems with electronic finders, or their DSLRs with second-sensor phase-detect AF modes, switchng between live view and viewfinder mode is a simple slide switch on top of the camera, with no performance degredation.

Using strictly the viewfinder, you should be able to obtain very accurate focus, as long as you don't move a hair from the time you achieve focus and trip the shutter. If you are using live view, there could be long delays which result in some minor movement, or discrepancies between the slow contrast-AF system if switching back to optical view before shooting...and depth of field cannot be accounted for unless you use DOF preview to confirm before shooting.

OK - for pure viewfinders, no...Sony's system at least on DSLRs is identical to most. Mirrors are most common for entry and mid level bodies, and pentaprisms for higher end and full frame cameras. Pentaprisms do not have the mirror, have much larger viewfinders, are usually much brighter and optically clearer, and usually show 100% framing or close to it.

Sony's SLTs which use the electronic viewfinders tend to have larger viewable field than most APS-C DSLRs - quite similar to full-frame pentaprisms in optical size - however are an electronic view as opposed to pure optical view, so you are looking through the sensor just as with live view, only through the viewfinder instead of on the LCD screen. This has some advantges and some disadvantages - which you'd want to consider before getting one. The types of shooting you do may play a part as to whether you want or need an optical finder or an electronic finder.